!  Assimilation Input parameters.
!
!svn $Id: assimilation.in 294 2009-01-09 21:37:26Z arango $
!========================================================= Hernan G. Arango ===
!  Copyright (c) 2002-2009 The ROMS/TOMS Group                                !
!    Licensed under a MIT/X style license                                     !
!    See License_ROMS.txt                                                     !
!==============================================================================
!                                                                             !
! Input parameters can be entered in ANY order, provided that the parameter   !
! KEYWORD (usually, upper case) is typed correctly followed by "="  or "=="   !
! symbols. Any comment lines are allowed and must begin with an exclamation   !
! mark (!) in column one.  Comments may  appear to the right of a parameter   !
! specification to improve documentation.  Comments will be ignored  during   !
! reading.  Blank lines are also allowed and ignored. Continuation lines in   !
! a parameter specification are allowed and must be preceded by a backslash   !
! (\).  In some instances, more than one value is required for a parameter.   !
! If fewer values are provided, the  last value  is assigned for the entire   !
! parameter array.  The multiplication symbol (*),  without blank spaces in   !
! between, is allowed for a parameter specification.  For example, in a two   !
! grids nested application:                                                   !
!                                                                             !
!    AKT_BAK == 2*1.0d-6  2*5.0d-6              ! m2/s                        !
!                                                                             !
! indicates that the first two entries of array AKT_BAK,  in fortran column-  !
! major order, will have the same value of "1.0d-6" for grid 1,  whereas the  !
! next two entries will have the same value of "5.0d-6" for grid 2.           !
!                                                                             !
! In multiple levels of nesting and/or multiple connected domains  step-ups,  !
! "Ngrids" entries are expected for some of these parameters.  In such case,  !
! the order of the entries for a parameter is extremely important.  It  must  !
! follow the same order (1:Ngrids) as in the state variable declaration. The  !
! USER may follow the above guidelines for specifying his/her values.  These  !
! parameters are marked by "==" plural symbol after the KEYWORD.              !
!                                                                             !
!==============================================================================
!
! Switch to control the data assimilation within nested and/or multiple
! connected grids, [1:Ngrids].

 Lassimilate == T

! Initial model error (percentage, 0-100%), [1:Ngrids].

       Emod0 == 50.0d0

! Empirical model error growth scale (days), [1:Ngrids].

     Tgrowth == 7.0d0

! Correlation between model and observations, [1:Ngrids].

         cor == 0.01d0

! Logical switches (T/F) to activate assimilation of requested fields,
! [1:Ngrids]

    assi_SSH == F                          ! sea surface height
    assi_SST == F                          ! sea surface temperature
  assi_UVsur == T                          ! surface U- and V-momentum
     assi_UV == F                          ! 3D U- and V-momentum
                       
! Logical switches (T/F) to activate assimilation of active tracers,
! temperature and salinity, [1:NAT,1:Ngrids].

      assi_T == T  T                       ! temperature and salinity

! Nudging assimilation time (days) scales. Inverse scales are computed
! internally, [1:Ngrids].

     Znudass == 0.0d0                      ! sea surface height
    M2nudass == 0.0d0                      ! 2D momentum
    M3nudass == 0.5d0                      ! 3D momentum

! Nudging ative tracers assimilation time (days) scales. Inverse scales are
! computed internally, [1:NAT,1:Ngrids].

     Tnudass == 0.5d0  0.5d0               ! temperature and salinity

! Extension parameters for sea surface temperature, [1:Ngrids].

  extend_SST == F                          ! logical switch
       ZmSST == -100.0d0                   ! maximum valid depth
       ZoSST == 5.0d0                      ! E-folding depth
       npSST == 0                          ! polynomial order

! Polynomial coefficients for sea surface temperature and its associated error
! variance extension.  The values must be entered using continuation lines.
! The first value in each line is the polynomial order whereas the second
! value is the polynomial coefficient. The values can be entered in any
! order, [0:npSST,1:Ngrids] values are expected.


   Pcoef_SST ==  GRID  ORDER        COEFFICIENT

                  1      0             0.0d0

    Perr_SST ==  GRID  ORDER        COEFFICIENT

                  1      0             0.0d0

! Extension parameters for surface velocity observations, [1:Ngrids].

   extend_UV == T                          ! logical switch
        ZmUV == -23.0d0                    ! maximum valid depth 
        ZoUV == 8.0d0                      ! E-folding depth
        npUV == 5                          ! polynomial order.

! Polynomial coefficients for momentum components and its associated error
! variance extension.  The values must be entered using continuation lines.
! The first value in each line is the polynomial order whereas the second
! value is the polynomial coefficient. The values can be entered in any
! order, [0:npUV,1:Ngrids] values are expected.

     Pcoef_U ==  GRID  ORDER        COEFFICIENT

                  1      0      6.594897011405828d-01
                  1      1     -4.849791482011837d-01
                  1      2     -4.005785294917267d+00
                  1      3     -1.102345420327383d+01
                  1      4     -1.312535632420359d+01
                  1      5     -5.176398126804888d+00 

     Pcoef_V ==  GRID  ORDER        COEFFICIENT

                  1      0     -1.217119523054544d-01
                  1      1     -4.800624107593688d-01
                  1      2     -4.905442938599552d+00
                  1      3     -1.578302790684537d+01
                  1      4     -1.675763388856354d+01
                  1      5     -5.683920816812656d+00

     Perr_UV ==  GRID  ORDER        COEFFICIENT

                  1      0      2.298160841773055e-01
                  1      1     -2.394646929016140e-01
                  1      2     -3.776174498462606e+00
                  1      3     -1.434422027381123e+01
                  1      4     -1.657203264674453e+01
                  1      5     -6.133984101209450e+00

! Input observations file names, if appicalble, [1:Ngrids].

     SSHname == oa_ssh.nc                  ! sea surface height
     SSTname == sst_ass.nc                 ! sea surface temperature
    VSURname == codar_ass.nc               ! surface currents, CODAR
    VOBSname == oa_adcp.nc                 ! 3D U- and V-momentum
    TOBSname == oa_tobs.nc                 ! temperature and salinity

!
!  GLOSSARY:
!  =========
!
!  Except for tracer related parameters and extension coefficients, (1:Ngrids)
!  values are expected for all parameters.
!
!------------------------------------------------------------------------------
! Assimilation control switch.
!------------------------------------------------------------------------------
!
! Lassimilate  Switch to control the data assimilation within nested and/or
!                multiple connected grids, [1:Ngrids].
!
!------------------------------------------------------------------------------
! Model error parameters.
!------------------------------------------------------------------------------
!
!  Emod0     Initial model error (percentage, 0-100%).
!
!  Tgrowth   Empirical model error growth scale (days).
!
!  cor       Correlation between model and observations.
!
!------------------------------------------------------------------------------
! Logical switches (T/F) to activate assimilation of requested fields.
!------------------------------------------------------------------------------
!
!  assi_SSH    Logical switch to assimilate sea surface height.
!
!  assi_SST    Logical switch to assimilate sea surface temperature.
!
!  assi_UVsur  Logical switch to assimilate surface U- and V-momentum.
!
!  assi_UV     Logical switch to assimilate 3D U- and V-momentum.
!
!  assi_T      Logical switch to assimilate tracer observations,
!                (1:NAT,1:Ngrids) tracers values are expected.
!
!------------------------------------------------------------------------------
! Nudging assimilation time (days) scales (inverse scales will be computed
! internally).
!------------------------------------------------------------------------------
!
!  Znudass     Nudging time scale (days) for free-surface.
!
!  M2nudass    Nudging time scale (days) for 2D momentum.
!
!  M3nudass    Nudging time scale (days) for 3D momentum.
!
!  Tnudass     Nudging time scale (days) for active tracer variables, 
!                (1:NAT,1:Ngrids) tracer values are expected.
!
!------------------------------------------------------------------------------
!  Extension parameters for sea surface temperature.
!------------------------------------------------------------------------------
!
! The extension is usually in term of EOF functions fitted to a polynomial
! of order npUV which is used to project vertically sea surface temperature 
! observations ant its associated error variance. The polynomial is a
! function of nondimensional depth z_r(:,:,k)/h(:,:), npSST+1 values are
! expected corresponding to ascending  powers of z_r/h (meters/meters;
! negative).
!
!  extend_SST  Logical switch to extend vertically sea surface temperature
!                observations before assiliation.
!
!  ZmSST       Maximum valid depth (meters) for sea surface temperature
!                extension basis function.  (OBSOLETE Parameter)
!
!  ZoSST       E-folding depth (m; positive) to extend vertically SST
!                nondimesional error variance. (OBSOLETE Parameter)
!
!  npSST       Order of the polynomial representing the basis functions
!                used for extension of sea surface temperature.
!
!  Pcoef_SST   Polynomial coefficients for sea surface temperature,
!                (0:npSST,1:Ngrids) values are expected.
!
!  Perr_SST    Polynomial coefficients for sea surface temperature error
!                variance, (0:npSST,1:Ngrids) values are expected.
!
!------------------------------------------------------------------------------
! Extension parameters for surface velocity observations.
!------------------------------------------------------------------------------
!
! The extension is usually in terms of EOF functions fitted to a polynomial
! of order npUV which is used to project vertically surface velocity 
! observations ant its associated error variance. The polynomial is a
! function of nondimensional depth z_r(:,:,k)/h(:,:), npUV+1 values are
! expected corresponding to ascending  powers of z_r/h (meters/meters;
! negative).
!
!  extend_UV   Logical switch to extend vertically surface velocity
!                observations before assiliation.
!
!  ZmUV        Maximum valid depth (meters) for surface velocity
!                extension basis functions. (OBSOLETE parameter)
!
!  ZoUV        E-folding depth (m; positive) to extend vertically
!                surface currents nondimesional error variance.
!                (OBSOLETE parameter).
!
!  npUV        Order of the polynomial representing the basis functions
!                used for extension of surface currents.
!
!  Pcoef_U     Polynomial coefficients for U-momentum component,
!                (0:npUV,1:Ngrids) values are expected.
!
!  Pcoef_V     Polynomial coefficients for V-momentum component,
!                (0:npUV,1:Ngrids) values are expected.
!
!  Perr_V      Polynomial coefficients for surface current error variance,
!                (0:npUV,1:Ngrids) values are expected.
!
!------------------------------------------------------------------------------
!  Input observations NetCDF files (a string with a maximum of eighty
!  characters).
!------------------------------------------------------------------------------
!
!  SSHname      Sea surface height observations file name, if any.
!
!  SSTname      Sea surface observation file name, if any.
!
!  VSURname     Surface currents observations file name, if any.
!
!  VOBSname     3D currents observations file name, if any.
!
!  TOBSname     Active tracer (temperature and salinity) observations
!                 file name, if any.
!
